Introduction and Overview1 1. Introduction and Overview 1.1. The Role of Soil Respiration in the Carbon Cycle The biogeochemical cycle of carbon includes several reservoirs which differ in their size and turnover times (Figure 1.1). The atmosphere holds about 800 gigatons (Gt) of carbon and has the fastest turnover time with ca. 122 Gt C being taken up by the terrestrial biosphere and 90-92 Gt C being exchanged with the surface ocean every year (Sabine et al. 2003).

Carbon can remain for a period of days to several years as part of the terrestrial biomass but will eventually be respired back to the atmosphere as CO , or it will become litter and 2 2 Soil Respiration Fluxes and Controlling Factors form part of the pedosphere, i.e. soils. Soils, with a total global storage of approximately 1500 Gt C (Jacobson et al. 2000) hold three times as much carbon as the terrestrial biosphere and about twice as much as the atmosphere. The carbon cycle is a dynamic system sensitive to environmental changes that can influence the magnitude of the fluxes and the storage time in each reservoir. Anthropogenic emission of CO from fossil fuels 2and land use change (e.g. deforestation, management) are currently driving this cycle away from equilibrium with largely unknown effects on the biosphere and the climate system, including positive and negative feedbacks. In order to understand and predict relations between the carbon cycle, vegetation and climate much effort is being directed towards understanding the processes involved. Soil respiration is defined as the efflux of CO from the soil surface and has been 2estimated at ca. 75-80 Gt of carbon per year globally (Raich and Potter 1995; Raich et al. 2002), which is nearly half of the gross primary productivity (GPP) of terrestrial ecosystems and about 10% of the total atmospheric carbon. Soil respiration is the result of the production of CO in soils from a combination of several belowground processes 2(Ryan and Law 2005; Trumbore 2006). The most important are the biological activity of roots and their associated microorganisms and the activity of heterotrophic bacteria and fungi living on litter and soil organic matter (SOM). Non biological processes related to -1chemical weathering in soils are estimated to be a net carbon sink of ca. 0.3 Gt yr (Jacobson et al. 2000), thus being of less significance. An increase in atmospheric CO concentrations has been identified as the main cause of 2current global warming (IPCC 2007). Given the magnitude of soil respiration fluxes, relatively small changes at the global scale can signify large changes in the amount of carbon stored in soils and in the atmosphere. A release of carbon from soils through respiration following climate change would create a positive feedback mechanism exacerbating warming effects. Conversely, increased storage of carbon in soils, as through CO fertilization of plant growth leading to increased inputs into soils, would 2imply a negative feedback and diminished warming effects. The implications of soil carbon dynamics for climate change are therefore of great importance, not only because of changes in storage, but also in relation to ecosystem physiology, acclimation and adaptation. Climate related changes in, for example, above and belowground CO2 Introduction and Overview3 concentrations, temperature changes, and water conditions will have yet largely unknown effects on respiration fluxes and carbon pools.These factors can affect carbon fluxes directly, as through temperature changes of enzymatic reaction rates (Davidson and Janssens 2006), but they may also have less direct effects through changes in vegetation, nutrient availability, etc. The cycling of carbon through soils is determined by vegetation and soil organic matter dynamics. Plant litter is the major source of soil organic matter. Litter quality and its processing by bacteria and fungi determine the size and properties of organic pools through interactions with soil minerals, soil structure and other soil characteristics (Kogel-Knabner 2002; Lutzow et al. 2006). At the same time, organic matter affects plant growth through its role in soil development and as a source of nutrients. The flow of carbon through soils is thus not a straightforward process. Temperature and moisture are known to have a large effect on the activity of roots and microbes. For soil microbes, higher temperatures may decrease the activation energy for degrading complex molecules and it may also lead to higher mobility of cells and organic matter, thus increasing respiration rates (Davidson et al. 2006). For roots, higher temperatures lead to increased maintenance respiration for repairing living tissues (Atkin et al. 2005). However, variations in soil respiration fluxes are not explained by temperatures and moisture alone. Relations of these fluxes with plant, rhizosphere, mycorrhizal and microbial dynamics and functioning, as well as with nutrients, organic matter, and soil characteristics, are currently being explored. The relevance of each factor and the relations involved are still not understood well enough to make long-term predictions of soil respiration with accuracy at local or global scales. The importance of C input by root and mycorrhiza in determining carbon storage in soils is likewise poorly characterized. As a consequence, soils are still a source of large uncertainty in ecosystem and climate modeling. 1.2. Measuring Soil Respiration The efflux of CO from soils is the result of the respiration of different groups of 2organisms, a fact which has lead to the development of methods to partition and measure these fluxes separately. These include trenching and exclusion, shading and clipping, 4 Soil Respiration Fluxes and Controlling Factors component integration, tree girdling and isotopic techniques. Comprehensive reviews of these methods are given by Hanson (2000), Kuzyakov and Larionova (2005), Kuzyakov (2006), and Subke (2006). Most methods involve a certain degree of disturbance of the soil system that changes natural fluxes to an uncertain degree. As an example, girdling of trees is an innovative method in which the sap flow from the canopy to the roots is cut, thus stopping the transport of new photosynthates without disturbing the soil system (Högberg et al. 2001). The dependence of belowground respiration activity on the short term supply of new carbon can thus be effectively studied. However, the use of reserve carbon stored in plant tissues and the decomposition of dying roots and mycorrhiza introduce uncertainties difficult to estimate. Isotopic techniques, on the other hand, present the lowest degree of disturbance (Gaudinski et al. 2000). However, isotope fractionation by different, sometimes unknown, processes creates further uncertainties, while the work and material involved in measuring isotopes also limits their applicability.

Figure 1.2: Diagram with a simplified representation of soil respiratory processes. For a more realistic view, a distinction is made between respiration by the live root tissue and respiration of rhizodeposits by microbes in the rhizosphere (rhizomicrobial respiration) and by mycorrhizal fungi (mycorrhizal respiration). Respiration of fresh plant litter is also distinguished from respiration of older, qualitatively different SOM (basal and priming respiration). Modified after Kuzyakov (2006). Introduction and Overview5

Despite the complications associatedwith different methods, partitioning soil respiration allows researchers to measure the contribution of each respiration source to total fluxes and the individual response of each source to environmental factors. Methods for partitioning frequently allow distinguishing between fluxes derived from root-carbon and those derived from soils without roots. Thus, the terms autotrophic soil respiration and heterotrophic soil respiration are widely used to distinguish between these sources. Other equivalent terms found in literature are root or rhizosphere respiration and microbial respiration. Studies using different methods have shown a different response of these fluxes to temperature and moisture conditions (Lavigne et al. 2003; Scott-Denton et al. 2006). Other partitioning studies have lead to a better understanding of the regulation of root respiration by plant functioning and phenology (Bahn et al. 2006; Fahey and Yavitt 2005). However, a closer view at the soil system shows that a simple partitioning in two components is not sufficient to explain carbon fluxes adequately. Factors such as root exudations, priming effects, symbiosis with mycorrhizal fungi, as well as differences in litter and SOM pools complicate the study of these fluxes. A more precise separation of belowground carbon fluxes becomes necessary, as shown in Figure 1.2. 1.3. Study Objectives The general aim of this study is to advance the understanding of processes controlling the activity of different belowground respiration sources at the ecosystem scale, as well as to identify relations that can serve as a basis for more realistic models and predictions of carbon fluxes. The specific objectives are:

• To partition soil respiration and to provide estimates of the relative contribution of respiration fluxes to total fluxes and their variability within and between different temperate ecosystems. • To determine the response of individual respiration fluxes to soil temperature and soil moisture, as well as to identify associated factors influencing such relations. 6 Soil Respiration Fluxes and Controlling Factors • To determine the effects of plant photosynthetic activity on rhizosphere and mycorrhizal fungi respiration, together with the time relations involved for each vegetation type. • To assess the specific spatial relation of individual respiration fluxes with relevant biological, chemical and physical soil parameters. 1.4. Study Approach and General Methodology The objectives of this study required a partitioning of soil respiration in multiple sites and measurements of different environmental variables influencing respiration fluxes. Although many points are described with more detail in the respective chapters, this section gives an overview and a description of the core methodology. Study Sites The study was carried out at the three main sites of the CarboEurope Integrated Project in Thuringia, Germany. This European project aims at quantifying and predicting carbon fluxes at the continental scale and relies on a number of measurement locations equipped with eddy covariance towers for determining CO exchange between the vegetation and 2the atmosphere (see below). The sites investigated are:

Gebesee: crop field with winter barley (Hordeum vulgare) during the study period

Hainich: old growth forest dominated by beech trees (Fagus sylvatica)

Wetzstein: 50 year old spruce (Picea abies) plantation forest

A more detailed description of each site can be found in the respective following chapters. Three main reasons were associated with choosing these locations. Firstly, these